From thamelry at vub.ac.be Mon Jul 1 03:31:28 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Why don't we start the documentations as well? In-Reply-To: References: Message-ID: <02070109312802.19705@imolpc112.vub.ac.be> [...] >For example, Once somebody learned how to use > BioPython and wants to use HMMs where does he go? The HMM module was not Happy Doc'ed for some reason. If it was, you would have a list of classes & methods etc. and a lot of documentation. I checked in the source code - it contains a lot of info. Simply applying Happy Doc would make that information readily available. I do not see any advantage in generating that info manually. Or am I missing something? > Currently he has to go to the source code No, you can check the API documentation generated with Happy Doc: http://www.biopython.org/wiki/html/BioPython/BiopythonCode.html > if we give him a reference he can simply look at the > classes, the different methods and understand how it works. Again, that list of classes and methods and a description of what they do and return can be generated automatically with Happy Doc. But maybe you are thinking of some kind of templated tutorial model? That would be useful IMO. In many cases a simple enumeration of classes & methods is not enough to use the package efficiently, so you need more. Cheers, -Thomas From thamelry at vub.ac.be Mon Jul 1 04:18:46 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] PDB again Message-ID: <02070110184604.19705@imolpc112.vub.ac.be> I added the PDB module documentation to the tutorial.tex file under "Advanced" - section 4.5. --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode, Belgium http://ultr.vub.ac.be/~thomas From Y.Benita at pharm.uu.nl Mon Jul 1 10:31:27 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Why don't we start the documentations as well? In-Reply-To: <02070109312802.19705@imolpc112.vub.ac.be> Message-ID: I guess its also fine, I don't have a preference as long as we get started on that. What do you think Jeff? Yair on 1/7/02 9:31, Thomas Hamelryck at thamelry@vub.ac.be wrote: > [...] > >> For example, Once somebody learned how to use >> BioPython and wants to use HMMs where does he go? > > The HMM module was not Happy Doc'ed for some reason. If it was, you would > have a list of classes & methods etc. and a lot of documentation. I checked > in the source code - it contains a lot of info. Simply applying Happy Doc > would make that information readily available. I do not see any advantage in > generating that info manually. Or am I missing something? > >> Currently he has to go to the source code > > No, you can check the API documentation generated with Happy Doc: > > http://www.biopython.org/wiki/html/BioPython/BiopythonCode.html > >> if we give him a reference he can simply look at the >> classes, the different methods and understand how it works. > > Again, that list of classes and methods and a description of what they do and > return can be generated automatically with Happy Doc. > > But maybe you are thinking of some kind of templated tutorial model? That > would be useful IMO. In many cases a simple enumeration of classes & methods > is not enough to use the package efficiently, so you need more. > > Cheers, > > -Thomas > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > From Y.Benita at pharm.uu.nl Mon Jul 1 10:37:59 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] PCR module In-Reply-To: Message-ID: on 29/5/02 8:29, Thomas Sicheritz-Ponten at thomas@cbs.dtu.dk wrote: > Ok, I am working on it! > Bio/SeqUtils/__init__.py So, how does it work? Should I send my scripts and you go through them and sort them out or would you prefer to define a strategy and I can fit the methods to that? I also have many PCR utilities including the extraction of exons from a given coding sequence (in case someone wants to use genomic DNA as a template). Will this be included in the SeqUtils module? Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University From chapmanb at arches.uga.edu Mon Jul 1 12:17:11 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Why don't we start the documentations as well? In-Reply-To: References: <02070109312802.19705@imolpc112.vub.ac.be> Message-ID: <20020701121711.A55477@ci350185-a.athen1.ga.home.com> Hey guys; Thomas: > >> For example, Once somebody learned how to use > >> BioPython and wants to use HMMs where does he go? > > > > The HMM module was not Happy Doc'ed for some reason. If it was, you would > > have a list of classes & methods etc. and a lot of documentation. I checked > > in the source code - it contains a lot of info. Simply applying Happy Doc > > would make that information readily available. I do not see any advantage in > > generating that info manually. Or am I missing something? Ugh, yeah, the HappyDoc documentation was badly out of date. I just updated everything so all the current classes should be included. If I missed something, please let me know! Yair: > I guess its also fine, I don't have a preference as long as we get started > on that. What do you think Jeff? More documentation is always better so whatever you want to work on is fine with me. The HappyDoc generated documentation is just a way to extract the classes and methods, and to get the comments from the source code; this way people can look at pretty HTML pages instead of the code if they like to. Personally, I wouldn't duplicate what HappyDoc gives, as that is a ton of pretty boring manual work and very tough to keep up to date by hand. But, any other documentation you want to work on is great! Brad -- PGP public key available from http://pgp.mit.edu/ From jchang at smi.stanford.edu Mon Jul 1 14:00:52 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Why don't we start the documentations as well? In-Reply-To: ; from Y.Benita@pharm.uu.nl on Mon, Jul 01, 2002 at 04:31:27PM +0200 References: <02070109312802.19705@imolpc112.vub.ac.be> Message-ID: <20020701110051.A99715@springfield.stanford.edu> On Mon, Jul 01, 2002 at 04:31:27PM +0200, Yair Benita wrote: > I guess its also fine, I don't have a preference as long as we get started > on that. What do you think Jeff? > Yair I like it. Either way is fine -- either beefing up the Happy doc documentation or working on a separate reference manual. Do you have a read/write CVS account, Yair? If you would like one to help with this, please send me you preferred account name and shell. Jeff From thamelry at vub.ac.be Mon Jul 1 15:28:40 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Why don't we start the documentations as well? Message-ID: <200207011925.g61JPY828769@excalibur.skynet.be> [Brad, on documentation] > Personally, I wouldn't duplicate what HappyDoc gives, as that is a ton > of pretty boring manual work and very tough to keep up to date by hand. > But, any other documentation you want to work on is great! What about manpage-like documentation for every module? That would be useful. These documents could have standard features like module name, author, synopsis, general use, usage examples, known bugs & limitations, implementation comments, related modules etc. That would complement the HappyDoc docs in a very nice way. Cheers, --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode Belgium http://ultr.vub.ac.be/~thomas From thamelry at vub.ac.be Mon Jul 1 15:29:28 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Why don't we start the documentations as well? Message-ID: <200207011926.g61JQLZ22090@picard.skynet.be> [Brad] > Ugh, yeah, the HappyDoc documentation was badly out of date. I just > updated everything so all the current classes should be included. If I > missed something, please let me know! Nice! One question/remark though: The structured text formatting rules at http://www.python.org/sigs/doc-sig/stext.html say that: Special symbology is used to indicate special constructs: * A paragraph that begins with a '-', '*', or 'o' is treated as an unordered list (bullet) element. (Note: In list paragraphs it is not necessary to separate each list item with a blank line.) This is supposed to apply to HappyDoc, but it doesn't happen, so you get funny stuff like: Arguments: o id - string, the id that will be used for the structure of o filename - name of the PDB file ie, there is no bulleted list. Maybe there is some option missing when running HappyDoc so that the docstrings are interpreted as plain text? Cheers, --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode Belgium http://ultr.vub.ac.be/~thomas From thamelry at vub.ac.be Tue Jul 2 08:39:02 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] KD tree module Message-ID: <200207021235.g62CZtZ00128@picard.skynet.be> Added regression test. The KD tree module now does: -Find all neighbors within radius r of given point p -Find all point pairs within radius r of each other It finds all bonds in the large ribosomal subunit (90000 atoms) in under 4 seconds. BTW, there a lot of Biopython tests that fail due to trivial reasons like: test test_ParserSupport failed -- Writing: 'Ran 3 tests in 0.005s', expected: 'Ran 3 tests in 0.111s' Cheers, --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode Belgium http://ultr.vub.ac.be/~thomas From jchang at smi.stanford.edu Wed Jul 3 03:51:35 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] KD tree module In-Reply-To: <200207021235.g62CZtZ00128@picard.skynet.be>; from thamelry@vub.ac.be on Tue, Jul 02, 2002 at 02:39:02PM +0200 References: <200207021235.g62CZtZ00128@picard.skynet.be> Message-ID: <20020703005135.A4968@springfield.stanford.edu> On Tue, Jul 02, 2002 at 02:39:02PM +0200, Thomas Hamelryck wrote: > BTW, there a lot of Biopython tests that fail due to trivial reasons like: > > test test_ParserSupport failed -- > Writing: 'Ran 3 tests in 0.005s', expected: 'Ran 3 tests in 0.111s' Hey, good catch. It looks like there's some testing code here that uses unittest.py, which writes out how long some code took. This is breaking from run to run. Is someone responsible for unittest.py? The easiest thing to do is to remove the verbiage that describes how long the tests took. The right thing to do would be to fix the two regression testing systems, but I suspect that would be too much work. What do people think? Jeff From thamelry at vub.ac.be Wed Jul 3 08:54:43 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] SVDSuperimposer Message-ID: <02070314544304.27461@imolpc112.vub.ac.be> Hey guys, Added Bio.Tools.SVDSuperimposer This module allows you to do a least-squares superposition of two coordinate sets. (It uses a singular value decomposition approach, hence SVDSuperimposer). Also added the corresponding test. You can use this e.g. to superimpose two crystal structures (if you have a set of equivalent atoms). Cheers, --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode, Belgium http://ultr.vub.ac.be/~thomas From chapmanb at arches.uga.edu Wed Jul 3 14:24:09 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Why don't we start the documentations as well? In-Reply-To: <200207011926.g61JQLZ22090@picard.skynet.be> References: <200207011926.g61JQLZ22090@picard.skynet.be> Message-ID: <20020703142409.D61366@ci350185-a.athen1.ga.home.com> [newly HappyDoc'ed biopython] Thomas: > One question/remark though: [...] > * A paragraph that begins with a '-', '*', or 'o' is treated as an unordered > list (bullet) element. (Note: In list paragraphs it is not necessary to > separate each list item with a blank line.) > > This is supposed to apply to HappyDoc, but it doesn't happen, so you get > funny stuff like: [...] > Maybe there is some option missing when running HappyDoc so that the > docstrings are interpreted as plain text? Actually, the problem is that HappyDoc treats things in a manner I didn't expect. In order to get a nice bulletted list you have to: * write the bullet points * with a space between each bullet point * which can get annoying if you have lots of bullet points * or just don't like have a million blank spaces in your comments Anyways, in the cases where it isn't processed, I probably either wrote it before I realized that you need the spaces or was just too annoyed to put in all that extra whitespace :-). I keep hoping that new releases of HappyDoc will clean this up so you can have nice tight lists and pretty generated documentation. In the meantime, I guess I just haven't figured out what too do :-). Brad -- PGP public key available from http://pgp.mit.edu/ From chapmanb at arches.uga.edu Wed Jul 3 14:27:20 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] KD tree module In-Reply-To: <20020703005135.A4968@springfield.stanford.edu> References: <200207021235.g62CZtZ00128@picard.skynet.be> <20020703005135.A4968@springfield.stanford.edu> Message-ID: <20020703142720.E61366@ci350185-a.athen1.ga.home.com> Thomas: > > BTW, there a lot of Biopython tests that fail due to trivial reasons like: > > > > test test_ParserSupport failed -- > > Writing: 'Ran 3 tests in 0.005s', expected: 'Ran 3 tests in 0.111s' Jeff: > Hey, good catch. It looks like there's some testing code here that > uses unittest.py, which writes out how long some code took. This is > breaking from run to run. I'm confused, I should have this all worked out, really :-) How are you guys running the tests? With current biopython CVS, I just do: [biopython]$ cd Tests [Tests]$ python run_tests.py --no-gui test_BioSQL ... ok and so on, and things work fine. Maybe I'm missing something or just crazy (or both!)? Brad -- PGP public key available from http://pgp.mit.edu/ From thamelry at vub.ac.be Wed Jul 3 16:26:12 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] KD tree module In-Reply-To: <20020703142720.E61366@ci350185-a.athen1.ga.home.com> References: <200207021235.g62CZtZ00128@picard.skynet.be> <20020703005135.A4968@springfield.stanford.edu> <20020703142720.E61366@ci350185-a.athen1.ga.home.com> Message-ID: <200207032023.g63KN4H11196@durendal.skynet.be> [Brad, about problems with the tests] > I'm confused, I should have this all worked out, really :-) > How are you guys running the tests? > > With current biopython CVS, I just do: > [biopython]$ cd Tests > [Tests]$ python run_tests.py --no-gui > test_BioSQL ... ok I was running "python br_regrtest.py" as suggested in http://www.biopython.org/wiki/html/BioPython/RegressionTests.html (and 25 tests failed). Is that documentation out-of-date? Sorry for causing panic! :-) When using "python run_tests.py" (almost) everything looks OK (FAIL: test_BioSQL, but that might be due to my setup, I guess). Cheers & thanks for the feedback, --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode Belgium http://ultr.vub.ac.be/~thomas From adalke at mindspring.com Wed Jul 3 16:26:37 2002 From: adalke at mindspring.com (Andrew Dalke) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] KD tree module In-Reply-To: <200207032023.g63KN4H11196@durendal.skynet.be> References: <200207021235.g62CZtZ00128@picard.skynet.be> <20020703005135.A4968@springfield.stanford.edu> <20020703142720.E61366@ci350185-a.athen1.ga.home.com> <200207032023.g63KN4H11196@durendal.skynet.be> Message-ID: <20020703142637.5b3f7454.adalke@mindspring.com> Thomas Hamelryck: > I was running "python br_regrtest.py" as suggested in > http://www.biopython.org/wiki/html/BioPython/RegressionTests.html > (and 25 tests failed). Is that documentation out-of-date? Sorry for causing > panic! :-) br_regrtest.py is quite out of date. I put it in based on some code I developed for Bioreason (hence the 'br') and some time before the now more standard Python code was available. Andrew From chapmanb at arches.uga.edu Fri Jul 5 09:20:26 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] KD tree module In-Reply-To: <200207032023.g63KN4H11196@durendal.skynet.be> References: <200207021235.g62CZtZ00128@picard.skynet.be> <20020703005135.A4968@springfield.stanford.edu> <20020703142720.E61366@ci350185-a.athen1.ga.home.com> <200207032023.g63KN4H11196@durendal.skynet.be> Message-ID: <20020705092026.B66018@ci350185-a.athen1.ga.home.com> [potential problems with the tests that had me all freaked out :-)] Thomas: > I was running "python br_regrtest.py" as suggested in > http://www.biopython.org/wiki/html/BioPython/RegressionTests.html > (and 25 tests failed). Is that documentation out-of-date? Sorry for causing > panic! :-) No worries :-). Sorry about the out of date documentation -- I've updated that page so that br_regrtest.py is no longer mentioned. Basically I rewrote br_regrtest.py into run_tests.py and added and modified things to fix some problems we were having with br_regrtest. We should get rid of br_regrtest sometime to get rid of confusion, but since it's Andrew's work I am afraid to delete it; I don't want him coming after me :-). > When using "python run_tests.py" (almost) everything looks OK (FAIL: > test_BioSQL, but that might be due to my setup, I guess). Great that most everything works! I'm not sure what the BioSQL problem is -- I would like it to fail gracefully in cases where people aren't setup for it; if you send the error I can try to mess with things so that it doesn't complain. Thanks for letting us know about the out of date docs! Brad -- PGP public key available from http://pgp.mit.edu/ From adalke at mindspring.com Fri Jul 5 12:09:14 2002 From: adalke at mindspring.com (Andrew Dalke) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] KD tree module In-Reply-To: <20020705092026.B66018@ci350185-a.athen1.ga.home.com> References: <200207021235.g62CZtZ00128@picard.skynet.be> <20020703005135.A4968@springfield.stanford.edu> <20020703142720.E61366@ci350185-a.athen1.ga.home.com> <200207032023.g63KN4H11196@durendal.skynet.be> <20020705092026.B66018@ci350185-a.athen1.ga.home.com> Message-ID: <20020705100914.2aa91013.adalke@mindspring.com> Brad Chapman: > Basically I rewrote br_regrtest.py into run_tests.py and added and > modified things to fix some problems we were having with br_regrtest. We > should get rid of br_regrtest sometime to get rid of confusion, but > since it's Andrew's work I am afraid to delete it; I don't want him > coming after me :-). No worries. Arm the venom gun and blast away. Oops! Have I been playing too much Return to Castle Wolfenstein? Andrew From thomas at cbs.dtu.dk Mon Jul 8 16:45:01 2002 From: thomas at cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Q: timetravel module In-Reply-To: matt cowan's message of "Mon, 20 May 2002 19:45:24 -0400" Message-ID: Hej, Does anybody have a copy of Tigran's timetravel module? I cannot access Tigran's server anymore (http://www.ocston.org/~tigran/tt/tt.html) - The new paup version(4b10) has a bootstrapping bug which makes it useless for me, so I need to be able to run the older version without setting the system for the whole server ... (I have mailed and asked paup support ... but as usual no answer) thx -thomas -- Sicheritz-Ponten Thomas, Ph.D, thomas@biopython.org ( Center for Biological Sequence Analysis \ BioCentrum-DTU, Technical University of Denmark ) CBS: +45 45 252485 Building 208, DK-2800 Lyngby ##-----> Fax: +45 45 931585 http://www.cbs.dtu.dk/thomas ) / ... damn arrow eating trees ... ( From biopython-bugs at bioperl.org Tue Jul 9 09:27:34 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Notification: incoming/74 Message-ID: <200207091327.g69DRYGV009808@pw600a.bioperl.org> JitterBug notification new message incoming/74 Message summary for PR#74 From: Oyvind.Edvardsen@hitos.no Subject: SwissProt parse error Date: Tue, 9 Jul 2002 09:27:33 -0400 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From Oyvind.Edvardsen@hitos.no Tue Jul 9 09:27:33 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g69DRXGV009802 for ; Tue, 9 Jul 2002 09:27:33 -0400 Date: Tue, 9 Jul 2002 09:27:33 -0400 Message-Id: <200207091327.g69DRXGV009802@pw600a.bioperl.org> From: Oyvind.Edvardsen@hitos.no To: biopython-bugs@bioperl.org Subject: SwissProt parse error Full_Name: Øyvind Edvardsen Module: SwissProt Version: biopython-1.00a4.win32-py2.2.exe OS: Win98SE Submission from: pc110-137.tromso.avidi.online.no (193.212.137.110) When parsing CCR4_HUMAN (P30991) from the current SwissProt release a SyntaxError exception is thrown at the RN [6] chunk of data. Apparently the parser expects to find only 1 line of RP data following. In this case (#6) the RP stuff continues on a second line. The error message shown is: Line does not start with RA. RP CORECEPTOR FUNCTION. Solution: allow RP to span more than 1 line. Keep up the good work! Øyvind E. From jchang at smi.stanford.edu Tue Jul 9 12:50:18 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Notification: incoming/74 In-Reply-To: <200207091327.g69DRYGV009808@pw600a.bioperl.org>; from biopython-bugs@bioperl.org on Tue, Jul 09, 2002 at 09:27:34AM -0400 References: <200207091327.g69DRYGV009808@pw600a.bioperl.org> Message-ID: <20020709095018.B22628@springfield.stanford.edu> Hello, Thanks for the bug report. This is fixed in the latest CVS version of the file. If you have not already fixed the bug, please download the SProt.py file from anonymous cvs. Jeff > >From Oyvind.Edvardsen@hitos.no Tue Jul 9 09:27:33 2002 > Received: from localhost (localhost [127.0.0.1]) > by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g69DRXGV009802 > for ; Tue, 9 Jul 2002 09:27:33 -0400 > Date: Tue, 9 Jul 2002 09:27:33 -0400 > Message-Id: <200207091327.g69DRXGV009802@pw600a.bioperl.org> > From: Oyvind.Edvardsen@hitos.no > To: biopython-bugs@bioperl.org > Subject: SwissProt parse error > > Full_Name: ?yvind Edvardsen > Module: SwissProt > Version: biopython-1.00a4.win32-py2.2.exe > OS: Win98SE > Submission from: pc110-137.tromso.avidi.online.no (193.212.137.110) > > > When parsing CCR4_HUMAN (P30991) from the > current SwissProt release a SyntaxError exception is thrown at the RN [6] > chunk of data. > Apparently the parser expects to find only 1 line of RP data following. In this > case (#6) the RP stuff continues on a second line. The error message shown is: > Line does not start with RA. > RP CORECEPTOR FUNCTION. > > Solution: allow RP to span more than 1 line. > > Keep up the good work! > > ?yvind E. > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From katel at worldpath.net Wed Jul 10 01:36:07 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] artificial immune system Message-ID: <003601c227d3$b1c29fa0$b470bbd1@pcklindner> I just committed a crude artificial immune system mostly to get the ball rolling on this technique. I invite everyone to play with it and come up with improvements. Cayte From thamelry at vub.ac.be Wed Jul 10 03:14:30 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] artificial immune system In-Reply-To: <003601c227d3$b1c29fa0$b470bbd1@pcklindner> References: <003601c227d3$b1c29fa0$b470bbd1@pcklindner> Message-ID: <02071009143000.29789@imolpc112.vub.ac.be> > I just committed a crude artificial immune system mostly to get the ball > rolling on this technique. I invite everyone to play with it and come up > with improvements. Sounds interesting. Could you give some more info? Where is it, what can you do with it, is there any documentation, any references? Cheers, --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode, Belgium http://ultr.vub.ac.be/~thomas From thamelry at vub.ac.be Wed Jul 10 05:13:52 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] More PDB stuff Message-ID: <02071011135204.29789@imolpc112.vub.ac.be> Added: NeighborSearch.py: Lookup of neighboring atoms, residues, etc.. Makes use of the KDTree module. Selection.py: This module does things like: get all residues that belong to a chain get all atoms that belong to a structure get all residues that contain given atoms etc. Regression tests follow later. Cheers, --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode, Belgium http://ultr.vub.ac.be/~thomas From katel at worldpath.net Wed Jul 10 16:20:47 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] artificial immune system References: <003601c227d3$b1c29fa0$b470bbd1@pcklindner> <02071009143000.29789@imolpc112.vub.ac.be> Message-ID: <001301c2284f$4875c3c0$bc72bbd1@pcklindner> > > I just committed a crude artificial immune system mostly to get the ball > > rolling on this technique. I invite everyone to play with it and come up > > with improvements. > > Sounds interesting. Could you give some more info? Where is it Under Bio.Ais I put in a little documentation. Under tests I have test_ais which shows how to construct it. , what can you > do with it, I threw it out on the basis of some articles. Its Experimental. I need to do experiments to see what it does . Hopefully it can learn stuff like to recognize corrupted strings. I'm off to the beach for a few days but I'll get to it. is there any documentation, any references? > > Cayte From biopython-bugs at bioperl.org Fri Jul 12 13:25:41 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Notification: incoming/75 Message-ID: <200207121725.g6CHPfYC027606@pw600a.bioperl.org> JitterBug notification new message incoming/75 Message summary for PR#75 From: daishi@egcrc.net Subject: Bio.Align.fastpairwise Date: Fri, 12 Jul 2002 13:25:40 -0400 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From daishi@egcrc.net Fri Jul 12 13:25:40 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g6CHPeYC027601 for ; Fri, 12 Jul 2002 13:25:40 -0400 Date: Fri, 12 Jul 2002 13:25:40 -0400 Message-Id: <200207121725.g6CHPeYC027601@pw600a.bioperl.org> From: daishi@egcrc.net To: biopython-bugs@bioperl.org Subject: Bio.Align.fastpairwise Full_Name: daishi Module: Bio.Align.fastpairwise Version: CVS v1.3 OS: linux Submission from: 63-193-205-1.egcrc.org (63.193.205.1) >>> from Bio.Align import fastpairwise >>> fastpairwise.align_local("abcde", "c", -0.3, -0.1) [('abcde', '--c--', 1, 1, 3)] The second to last field in the response should be 2, I think. When there are multiple matches only one match exhibits this behavior: >>> fastpairwise.align_local("abcce", "c", -0.3, -0.1) [('abcce', '---c-', 1, 1, 4), ('abcce', '--c--', 1, 2, 3)] I traced some of the code execution and found that the cached results return the correct response, but the original traceback is doing something incorrect. From daishi at egcrc.net Mon Jul 15 19:15:44 2002 From: daishi at egcrc.net (daishi@egcrc.net) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Follow up to bug incoming/75 Message-ID: <3D3357A0.3040806@egcrc.net> I believe that the following patch fixes the problem that I mentioned in the bug report (side note: I couldn't seem to find a way to follow up on the bug report through the web interface provided - did I miss something?) I'm not entirely sure that I understood all of the code, however, so please consider the patch with that in mind. In particular, I didn't entirely understand the code at L332-333 in the CVS version 1.3 of fastpairwise.py. I had to comment them out in my patch to get things to work properly. Daishi *** /usr/local/src/biopython/Bio/Align/fastpairwise.py Tue Jul 9 15:08:53 2002 --- fastpairwise.py Mon Jul 15 16:03:05 2002 *************** *** 302,308 **** else: # Since the length of the alignment is unknown, set an # offset from the end of the alignment. ! begin, end = 0, -len(seqA) if not end: end = None x = seqA, seqB, score, begin, end, row, col, [] --- 302,308 ---- else: # Since the length of the alignment is unknown, set an # offset from the end of the alignment. ! begin, end = None, -len(seqA) if not end: end = None x = seqA, seqB, score, begin, end, row, col, [] *************** *** 329,341 **** nbegin = begin nseqA = cseqA[:-taillen] + seqA nseqB = cseqB[:-taillen] + seqB ! if nbegin < cbegin: ! nbegin = cbegin x = nseqA, nseqB, score, nbegin, end, -1, -1, path in_process.append(x) elif row < 0 and col < 0: # This one is done. Put it into the tracebacks list and # continue. tracebacks.append((seqA, seqB, score, begin, end)) path.pop() # Don't cache the last step. # Update the cache. --- 329,343 ---- nbegin = begin nseqA = cseqA[:-taillen] + seqA nseqB = cseqB[:-taillen] + seqB ! # if nbegin < cbegin: ! # nbegin = cbegin x = nseqA, nseqB, score, nbegin, end, -1, -1, path in_process.append(x) elif row < 0 and col < 0: # This one is done. Put it into the tracebacks list and # continue. + if not begin: + begin = 0 tracebacks.append((seqA, seqB, score, begin, end)) path.pop() # Don't cache the last step. # Update the cache. *************** *** 347,360 **** elif row < 0: nseqA = gap_char + seqA nseqB = sequenceB[col:col+1] + seqB ! if not global_alignment: begin = col + 1 x = nseqA, nseqB, score, begin, end, row, col-1, path in_process.append(x) elif col < 0: nseqA = sequenceA[row:row+1] + seqA nseqB = gap_char + seqB ! if not global_alignment: begin = row + 1 x = nseqA, nseqB, score, begin, end, row-1, col, path in_process.append(x) --- 349,362 ---- elif row < 0: nseqA = gap_char + seqA nseqB = sequenceB[col:col+1] + seqB ! if not (global_alignment or begin): begin = col + 1 x = nseqA, nseqB, score, begin, end, row, col-1, path in_process.append(x) elif col < 0: nseqA = sequenceA[row:row+1] + seqA nseqB = gap_char + seqB ! if not (global_alignment or begin): begin = row + 1 x = nseqA, nseqB, score, begin, end, row-1, col, path in_process.append(x) From gec at threeplusone.com Mon Jul 15 19:43:19 2002 From: gec at threeplusone.com (Gavin Crooks) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Failed Tests Message-ID: A bunch of biopython tests are failing or being skipped on my machine. Anyone know whats up? Gavin test_Crystal ... Skipping test because of import error: No module named Hetero ok test_KDTree ... Skipping test because of import error: No module named _KDTreecok test_cdd ... Skipping test because of import error: cannot import name remove_leading_whitespace test_ndb ... Skipping test because of import error: cannot import name Hetero ====================================================================== FAIL: test_BioSQL ---------------------------------------------------------------------- Traceback (most recent call last): File "run_tests.py", line 131, in runTest self.runSafeTest() File "run_tests.py", line 168, in runSafeTest expected_handle) File "run_tests.py", line 268, in compare_output assert expected_line == output_line, \ AssertionError: Output : 'Load SeqRecord objects into a BioSQL database. ... ERROR\n' Expected: 'Load SeqRecord objects into a BioSQL database. ... ok\n' ====================================================================== FAIL: test_align ---------------------------------------------------------------------- Traceback (most recent call last): File "run_tests.py", line 131, in runTest self.runSafeTest() File "run_tests.py", line 168, in runSafeTest expected_handle) File "run_tests.py", line 268, in compare_output assert expected_line == output_line, \ AssertionError: Output : 'testing reading and writing fasta format...\n' Expected: '0 T 2.000\n' ---------------------------------------------------------------------- Ran 60 tests in 187.649s From katel at worldpath.net Tue Jul 16 00:09:37 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Failed Tests References: Message-ID: <000a01c22c7e$9ad75560$08fea8c0@pcklindner> I made the changes so it shud work. Let me know. I'll be online till way late. Cayte From katel at worldpath.net Tue Jul 16 00:10:03 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Failed Tests References: Message-ID: <000d01c22c7e$aa2a5e40$08fea8c0@pcklindner> > > test_Crystal ... Skipping test because of import error: No module named > Hetero > ok I migrated Hetro to the __init__ file. I need to check in the change. The dangling reference worked on my system because I didn't delete the old Hetero. > test_KDTree ... Skipping test because of import error: No module named > _KDTreecok > test_cdd ... Skipping test because of import error: cannot import name > remove_leading_whitespace Seems I added this since the last commit > test_ndb ... Skipping test because of import error: cannot import name > Hetero Same as Hetero > Let me know how it goes when I check the changes in. Cayte From gec at threeplusone.com Mon Jul 15 21:24:24 2002 From: gec at threeplusone.com (Gavin Crooks) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Failed Tests Message-ID: Test_KDTree is still skipped, and test_ndb now runs, but fails.. FAIL: test_ndb ---------------------------------------------------------------------- Traceback (most recent call last): File "run_tests.py", line 131, in runTest self.runSafeTest() File "run_tests.py", line 168, in runSafeTest expected_handle) File "run_tests.py", line 268, in compare_output assert expected_line == output_line, \ AssertionError: Output : 'Sequence: F : g c g a t a t a c g u\n' Expected: 'Sequence: A : g c g a t a t a c g u\n' ---------------------------------------------------------------------- Ran 60 tests in 164.546s > > > > test_Crystal ... Skipping test because of import error: No module named > > Hetero > > ok > > I migrated Hetro to the __init__ file. I need to check in the change. > The dangling reference worked on my system because I didn't delete the old > Hetero. > > > test_KDTree ... Skipping test because of import error: No module named > > _KDTreecok > > test_cdd ... Skipping test because of import error: cannot import name > > remove_leading_whitespace > Seems I added this since the last commit > > test_ndb ... Skipping test because of import error: cannot import name > > Hetero > Same as Hetero > > > Let me know how it goes when I check the changes in. > > Cayte > > > From katel at worldpath.net Tue Jul 16 00:50:03 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Failed Tests References: Message-ID: <001901c22c84$406596e0$08fea8c0@pcklindner> OOps. Looks like a missing sort. I checked in the change. Cayte From jchang at smi.stanford.edu Tue Jul 16 03:32:16 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Follow up to bug incoming/75 In-Reply-To: <3D3357A0.3040806@egcrc.net>; from daishi@egcrc.net on Mon, Jul 15, 2002 at 04:15:44PM -0700 References: <3D3357A0.3040806@egcrc.net> Message-ID: <20020716003216.B41639@springfield.stanford.edu> Hi Daishi, Thanks for the bug report and patch. I will look into this soon. Jeff On Mon, Jul 15, 2002 at 04:15:44PM -0700, daishi@egcrc.net wrote: > I believe that the following patch fixes the problem that > I mentioned in the bug report (side note: I couldn't seem > to find a way to follow up on the bug report through the > web interface provided - did I miss something?) > > I'm not entirely sure that I understood all of the code, > however, so please consider the patch with that in mind. > In particular, I didn't entirely understand the code at > L332-333 in the CVS version 1.3 of fastpairwise.py. > I had to comment them out in my patch to get things to > work properly. > > Daishi > > > *** /usr/local/src/biopython/Bio/Align/fastpairwise.py Tue Jul 9 15:08:53 2002 > --- fastpairwise.py Mon Jul 15 16:03:05 2002 > *************** > *** 302,308 **** > else: > # Since the length of the alignment is unknown, set an > # offset from the end of the alignment. > ! begin, end = 0, -len(seqA) > if not end: > end = None > x = seqA, seqB, score, begin, end, row, col, [] > --- 302,308 ---- > else: > # Since the length of the alignment is unknown, set an > # offset from the end of the alignment. > ! begin, end = None, -len(seqA) > if not end: > end = None > x = seqA, seqB, score, begin, end, row, col, [] > *************** > *** 329,341 **** > nbegin = begin > nseqA = cseqA[:-taillen] + seqA > nseqB = cseqB[:-taillen] + seqB > ! if nbegin < cbegin: > ! nbegin = cbegin > x = nseqA, nseqB, score, nbegin, end, -1, -1, path > in_process.append(x) > elif row < 0 and col < 0: > # This one is done. Put it into the tracebacks list and > # continue. > tracebacks.append((seqA, seqB, score, begin, end)) > path.pop() # Don't cache the last step. > # Update the cache. > --- 329,343 ---- > nbegin = begin > nseqA = cseqA[:-taillen] + seqA > nseqB = cseqB[:-taillen] + seqB > ! # if nbegin < cbegin: > ! # nbegin = cbegin > x = nseqA, nseqB, score, nbegin, end, -1, -1, path > in_process.append(x) > elif row < 0 and col < 0: > # This one is done. Put it into the tracebacks list and > # continue. > + if not begin: > + begin = 0 > tracebacks.append((seqA, seqB, score, begin, end)) > path.pop() # Don't cache the last step. > # Update the cache. > *************** > *** 347,360 **** > elif row < 0: > nseqA = gap_char + seqA > nseqB = sequenceB[col:col+1] + seqB > ! if not global_alignment: > begin = col + 1 > x = nseqA, nseqB, score, begin, end, row, col-1, path > in_process.append(x) > elif col < 0: > nseqA = sequenceA[row:row+1] + seqA > nseqB = gap_char + seqB > ! if not global_alignment: > begin = row + 1 > x = nseqA, nseqB, score, begin, end, row-1, col, path > in_process.append(x) > --- 349,362 ---- > elif row < 0: > nseqA = gap_char + seqA > nseqB = sequenceB[col:col+1] + seqB > ! if not (global_alignment or begin): > begin = col + 1 > x = nseqA, nseqB, score, begin, end, row, col-1, path > in_process.append(x) > elif col < 0: > nseqA = sequenceA[row:row+1] + seqA > nseqB = gap_char + seqB > ! if not (global_alignment or begin): > begin = row + 1 > x = nseqA, nseqB, score, begin, end, row-1, col, path > in_process.append(x) > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From daishi at egcrc.net Tue Jul 16 18:23:46 2002 From: daishi at egcrc.net (daishi@egcrc.net) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Follow up to bug incoming/75 References: <3D3357A0.3040806@egcrc.net> <20020716003216.B41639@springfield.stanford.edu> Message-ID: <3D349CF2.9030009@egcrc.net> Jeffrey Chang wrote: > Hi Daishi, > > Thanks for the bug report and patch. I will look into this soon. > > Jeff Please ignore the previous patch; it contains a bug. I believe I now understand the purpose of L332-333; I have reincorporated the functionality in a slightly different way which works with my other modifications. The new patch follows: *** /usr/local/src/biopython/Bio/Align/fastpairwise.py Tue Jul 9 15:08:53 2002 --- fastpairwise.py Tue Jul 16 15:15:50 2002 *************** *** 302,308 **** else: # Since the length of the alignment is unknown, set an # offset from the end of the alignment. ! begin, end = 0, -len(seqA) if not end: end = None x = seqA, seqB, score, begin, end, row, col, [] --- 302,308 ---- else: # Since the length of the alignment is unknown, set an # offset from the end of the alignment. ! begin, end = None, -len(seqA) if not end: end = None x = seqA, seqB, score, begin, end, row, col, [] *************** *** 326,341 **** elif col < 0: begin = row + 1 for cseqA, cseqB, cbegin, taillen in path_cache[(row, col)]: ! nbegin = begin nseqA = cseqA[:-taillen] + seqA nseqB = cseqB[:-taillen] + seqB ! if nbegin < cbegin: ! nbegin = cbegin x = nseqA, nseqB, score, nbegin, end, -1, -1, path in_process.append(x) elif row < 0 and col < 0: # This one is done. Put it into the tracebacks list and # continue. tracebacks.append((seqA, seqB, score, begin, end)) path.pop() # Don't cache the last step. # Update the cache. --- 326,346 ---- elif col < 0: begin = row + 1 for cseqA, cseqB, cbegin, taillen in path_cache[(row, col)]: ! if begin: ! nbegin = begin ! else: ! nbegin = cbegin nseqA = cseqA[:-taillen] + seqA nseqB = cseqB[:-taillen] + seqB ! # if nbegin < cbegin: ! # nbegin = cbegin x = nseqA, nseqB, score, nbegin, end, -1, -1, path in_process.append(x) elif row < 0 and col < 0: # This one is done. Put it into the tracebacks list and # continue. + if not begin: + begin = 0 tracebacks.append((seqA, seqB, score, begin, end)) path.pop() # Don't cache the last step. # Update the cache. *************** *** 347,360 **** elif row < 0: nseqA = gap_char + seqA nseqB = sequenceB[col:col+1] + seqB ! if not global_alignment: begin = col + 1 x = nseqA, nseqB, score, begin, end, row, col-1, path in_process.append(x) elif col < 0: nseqA = sequenceA[row:row+1] + seqA nseqB = gap_char + seqB ! if not global_alignment: begin = row + 1 x = nseqA, nseqB, score, begin, end, row-1, col, path in_process.append(x) --- 352,365 ---- elif row < 0: nseqA = gap_char + seqA nseqB = sequenceB[col:col+1] + seqB ! if not (global_alignment or begin): begin = col + 1 x = nseqA, nseqB, score, begin, end, row, col-1, path in_process.append(x) elif col < 0: nseqA = sequenceA[row:row+1] + seqA nseqB = gap_char + seqB ! if not (global_alignment or begin): begin = row + 1 x = nseqA, nseqB, score, begin, end, row-1, col, path in_process.append(x) From katel at worldpath.net Wed Jul 17 00:16:15 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Failed Tests References: Message-ID: <002601c22d48$b28a52a0$08fea8c0@pcklindner> I'm concerned because the fourmilab random number site seems to be down tonight so tests of programs that use it ( Ais and HotRand ) won't work. For the future maybe I could force a bunch of vals into the cache next time the server is up to protect against server problems. Cayte From jchang at smi.stanford.edu Tue Jul 16 21:26:01 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Failed Tests In-Reply-To: <002601c22d48$b28a52a0$08fea8c0@pcklindner>; from katel@worldpath.net on Tue, Jul 16, 2002 at 09:16:15PM -0700 References: <002601c22d48$b28a52a0$08fea8c0@pcklindner> Message-ID: <20020716182601.A44067@springfield.stanford.edu> Since many people won't have net connections all the time, the regression tests shouldn't require there to be a net connection. I have submitted a bug report for augmenting the regression testing framework that gracefully handle times when the internet is unavailable. http://cvs.bioperl.org/bugzilla/show_bug.cgi?id=6 All core developers should create accounts on the experimental Bugzilla database at http://cvs.bioperl.org/bugzilla. Jeff On Tue, Jul 16, 2002 at 09:16:15PM -0700, Cayte wrote: > I'm concerned because the fourmilab random number site seems to be down > tonight so tests of programs that use it ( Ais and HotRand ) won't work. > For the future maybe I could force a bunch of vals into the cache next time > the server is up to protect against server problems. > > Cayte > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From adalke at mindspring.com Wed Jul 17 02:09:27 2002 From: adalke at mindspring.com (Andrew Dalke) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] structure BoF at BOISC 2002 In-Reply-To: <02061715541009.29122@imolpc112.vub.ac.be> References: <02061715541009.29122@imolpc112.vub.ac.be> Message-ID: <20020717000927.382898e7.adalke@mindspring.com> BTW, there will be a Structure BoF at BOSC to talk about how to store and manipulate macromolecular structure. Andrew From thamelry at vub.ac.be Wed Jul 17 05:21:34 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] structure BoF at BOISC 2002 In-Reply-To: <20020717000927.382898e7.adalke@mindspring.com> References: <02061715541009.29122@imolpc112.vub.ac.be> <20020717000927.382898e7.adalke@mindspring.com> Message-ID: <02071711213403.05473@imolpc112.vub.ac.be> > BTW, there will be a Structure BoF at BOSC to talk about how > to store and manipulate macromolecular structure. I can't be there, but I'd be interested in hearing what was said. -Thomas --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode, Belgium http://ultr.vub.ac.be/~thomas From desas2 at excsrv38.mayo.edu Wed Jul 17 17:22:39 2002 From: desas2 at excsrv38.mayo.edu (Dinakar) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] is there any problem with GenBank FeatureParser In-Reply-To: <002601c22d48$b28a52a0$08fea8c0@pcklindner> Message-ID: Hello: I have installed biopython 1.04a and python 2.2.1. I am trying to go through tutorials and also tutorial from Pasteur institute. In section of 3.4.1 they use GenBank FeatureParser. I tried to use it and it gives lots of traceback. I would appreciate, if any of you could help with this. Thank you. Dinakar from Bio import GenBank record_parser = GenBank.FeatureParser() ncbi_dict = GenBank.NCBIDictionary(parser = record_parser) gb_seqrecord = ncbi_dict['5595'] print gb_seqrecord Traceback (most recent call last): File "./test_as.py", line 32, in ? gb_seqrecord = ncbi_dict['5595'] File "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 1555, in __getitem__ return self.parser.parse(handle) File "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 268, in parse self._scanner.feed(handle, self._consumer) File "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 1250, in feed self._parser.parseFile(handle) File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", line 230, in parseFile self.parseString(fileobj.read()) File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", line 258, in parseString self._err_handler.fatalError(result) File "/home/desas2/lib/python2.2/xml/sax/handler.py", line 38, in fatalError raise exception Martel.Parser.ParserPositionException: error parsing at or beyond character 55 From thamelry at vub.ac.be Thu Jul 18 06:02:16 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:14 2005 Subject: [Biopython-dev] Re: [BioPython] martel & mindy In-Reply-To: <4613E4C3-99E8-11D6-A5A9-00039390F614@anu.edu.au> References: <4613E4C3-99E8-11D6-A5A9-00039390F614@anu.edu.au> Message-ID: <02071812021602.10591@imolpc112.vub.ac.be> > Oooh, can I do that with PDB? Can anyone point me to documentation? What exactly do you want to do? > I have the CVS version of BioPython with PDB parser but don't know much > about its internals yet. It only parses the atomic data and puts this in a nice hierarchical data structure (Structure-Model-Chain-Residue-Atom). It doesn't look at the PDB header at all. I assume you want to get info from the header. As far as I can see it does not make much sense to do the parsing of the atomic data with Martel. Martel would be excellent to parse the header. > It is also pretty slow with big records, and > building an index on just a few fields would be really useful. Slow? It builds a full SMCRA datastructure+sanity checking in 3s for an 11000 atom structure. That's quite OK I think! Of course that's completely unimpressive if you need data from the header.... Cheers, --- Thomas Hamelryck Vrije Universiteit Brussel (VUB) Intitute for Molecular Biology ULTR Department Paardenstraat 65 1640 Sint-Gensius-Rode, Belgium http://ultr.vub.ac.be/~thomas From thamelry at vub.ac.be Thu Jul 18 06:02:55 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] Added NN search Message-ID: <02071812025503.10591@imolpc112.vub.ac.be> Hi Andrew, Thanks for the feedback on the KD tree. > Is this really the case that it takes 3/4 of a minute to > do a distance search on 10,000 points? That was some time ago. I was also surprised that it was so slow, so I took a good look at my algorithm and discovered that I was examining waaaay to many tree nodes. It's much faster now. BTW, the 45s was for finding all point pairs within radius r of each other, not for an individual query. Running a program that fills a 1x1x1 box with 100.000 random points and then finds all point pairs within a radius of 0.01 (typically 20.000 pairs) now takes 7s (time python __init__.py in the KDTree directory) on my 1 GHz. > BTW, I had some problems understanding the API. See the attachment > where I commented out what doesn't work. You have used the raw SWIG generated module! There's another layer on top of that, which does more error checking etc. It should not be possible e.g. to get segfaults with that module. In short: from Bio.Tools.KDTree import KDTree kdt=KDTree(dim, bucketsize) kdt.set_coords(coords) # individual queries kdt.search(center, radius) kdt.get_indices() kdt.get_radii() # al pairs kdt.all_search(radius) kdt.all_get_indices() kdt.all_get_radii() The __init__.py file in the KDTree dirctory now contains an example of howto use the module. > One of the things people want is to find the all the points in > set X which are within distance r of any point in set Y. True. I didn't really think of that. For X small and Y large you can build a KD tree for Y and query the tree with the positions in X. For X and Y large you can lump them together, build a KD tree, do an all-neighbors search and filter the results. Maybe I can come up with a nicer solution for that last case. 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------=_NextPart_84815C5ABAF209EF376268C8-- From thamelry at vub.ac.be Thu Jul 18 07:38:38 2002 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] Added NN search In-Reply-To: <20020718021413.03b78768.adalke@mindspring.com> References: <200206210959.g5L9xY929824@riker.skynet.be> <20020718021413.03b78768.adalke@mindspring.com> Message-ID: <02071813383807.10591@imolpc112.vub.ac.be> > One of the things people want is to find the all the points in > set X which are within distance r of any point in set Y. I thought about it - it should be fairly easy to adapt the all-neighbor search algorithm for this type of query as well. Should be very fast. It's on the to-do list. -Thomas From Desai.Dinakar at mayo.edu Thu Jul 18 12:02:41 2002 From: Desai.Dinakar at mayo.edu (Dinakar Desai) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] need help with Genbank Message-ID: <3D36E6A1.1060509@mayo.edu> Hello: I have install biopython1.004a and python 2.2.1 on linux box. I am going through tutorial written by Brad et al. (very good work). With following code I get trace back which I have pasted at the end. Can someone help me with. I must be dong something wrong here. Thanks Dinakar 30 from Bio import GenBank 31 record_file = open('record_file.seq', 'w+') 32 record_parser = GenBank.FeatureParser() 33 ncbi_dict = GenBank.NCBIDictionary() 34 for id in titles: 35 gb_seqrecord = ncbi_dict[id] 36 record_file.write( gb_seqrecord) 37 38 39 record_file.close() 40 record_file = open('record_file.seq', 'r') 41 gb_iter = GenBank.Iterator(record_file, record_parser) 42 while 1: 43 current_record = gb_iter.next() 44 if current_record is None: 45 break 46 print current_record.seq 47 print current_record.source 48 print current_record.author 49 record_file.close() Traceback (most recent call last): File "./test_as.py", line 43, in ? current_record = gb_iter.next() File "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", linet return self._parser.parse(File.StringHandle(data)) File "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", linee self._scanner.feed(handle, self._consumer) File "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", lined self._parser.parseFile(handle) File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", line 230, ie self.parseString(fileobj.read()) File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", line 258, ig self._err_handler.fatalError(result) File "/home/desas2/lib/python2.2/xml/sax/handler.py", line 38, in fatalError raise exception Martel.Parser.ParserPositionException: error parsing at or beyond character 55 -- From jchang at smi.stanford.edu Thu Jul 18 12:19:01 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] need help with Genbank In-Reply-To: <3D36E6A1.1060509@mayo.edu>; from Desai.Dinakar@mayo.edu on Thu, Jul 18, 2002 at 11:02:41AM -0500 References: <3D36E6A1.1060509@mayo.edu> Message-ID: <20020718091900.B48356@springfield.stanford.edu> The GenBank parser has gone through a few revisions to handle format changes since 1.00a4 was released. Try getting the latest version out of CVS (cvs.open-bio.org) and see if that fixes the problem. Otherwise, please send in a sample GenBank record that causes the parser to break. Jeff On Thu, Jul 18, 2002 at 11:02:41AM -0500, Dinakar Desai wrote: > Hello: > > I have install biopython1.004a and python 2.2.1 on linux box. I am going > through tutorial written by Brad et al. (very good work). > With following code I get trace back which I have pasted at the end. > Can someone help me with. I must be dong something wrong here. > > Thanks > > Dinakar > > 30 from Bio import GenBank > 31 record_file = open('record_file.seq', 'w+') > 32 record_parser = GenBank.FeatureParser() > 33 ncbi_dict = GenBank.NCBIDictionary() > 34 for id in titles: > 35 gb_seqrecord = ncbi_dict[id] > 36 record_file.write( gb_seqrecord) > 37 > 38 > 39 record_file.close() > 40 record_file = open('record_file.seq', 'r') > 41 gb_iter = GenBank.Iterator(record_file, record_parser) > 42 while 1: > 43 current_record = gb_iter.next() > 44 if current_record is None: > 45 break > 46 print current_record.seq > 47 print current_record.source > 48 print current_record.author > 49 record_file.close() > > > > Traceback (most recent call last): > File "./test_as.py", line 43, in ? > current_record = gb_iter.next() > File > "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", linet > return self._parser.parse(File.StringHandle(data)) > File > "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", linee > self._scanner.feed(handle, self._consumer) > File > "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", lined > self._parser.parseFile(handle) > File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", > line 230, ie > self.parseString(fileobj.read()) > File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", > line 258, ig > self._err_handler.fatalError(result) > File "/home/desas2/lib/python2.2/xml/sax/handler.py", line 38, in > fatalError > raise exception > Martel.Parser.ParserPositionException: error parsing at or beyond > character 55 > > > -- > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From Desai.Dinakar at mayo.edu Thu Jul 18 13:26:56 2002 From: Desai.Dinakar at mayo.edu (Dinakar Desai) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] need help with Genbank References: <3D36E6A1.1060509@mayo.edu> <20020718091900.B48356@springfield.stanford.edu> Message-ID: <3D36FA60.5080402@mayo.edu> Jeffrey Chang wrote: > The GenBank parser has gone through a few revisions to handle format > changes since 1.00a4 was released. Try getting the latest version out > of CVS (cvs.open-bio.org) and see if that fixes the problem. > > Otherwise, please send in a sample GenBank record that causes the > parser to break. > > Jeff > > > > > On Thu, Jul 18, 2002 at 11:02:41AM -0500, Dinakar Desai wrote: > >>Hello: >> >>I have install biopython1.004a and python 2.2.1 on linux box. I am going >>through tutorial written by Brad et al. (very good work). >>With following code I get trace back which I have pasted at the end. >>Can someone help me with. I must be dong something wrong here. >> >>Thanks >> >>Dinakar >> >> 30 from Bio import GenBank >> 31 record_file = open('record_file.seq', 'w+') >> 32 record_parser = GenBank.FeatureParser() >> 33 ncbi_dict = GenBank.NCBIDictionary() >> 34 for id in titles: >> 35 gb_seqrecord = ncbi_dict[id] >> 36 record_file.write( gb_seqrecord) >> 37 >> 38 >> 39 record_file.close() >> 40 record_file = open('record_file.seq', 'r') >> 41 gb_iter = GenBank.Iterator(record_file, record_parser) >> 42 while 1: >> 43 current_record = gb_iter.next() >> 44 if current_record is None: >> 45 break >> 46 print current_record.seq >> 47 print current_record.source >> 48 print current_record.author >> 49 record_file.close() >> >> >> >>Traceback (most recent call last): >> File "./test_as.py", line 43, in ? >> current_record = gb_iter.next() >> File >>"/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", linet >> return self._parser.parse(File.StringHandle(data)) >> File >>"/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", linee >> self._scanner.feed(handle, self._consumer) >> File >>"/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", lined >> self._parser.parseFile(handle) >> File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", >>line 230, ie >> self.parseString(fileobj.read()) >> File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", >>line 258, ig >> self._err_handler.fatalError(result) >> File "/home/desas2/lib/python2.2/xml/sax/handler.py", line 38, in >>fatalError >> raise exception >>Martel.Parser.ParserPositionException: error parsing at or beyond >>character 55 >> >> >>-- >> >> >>_______________________________________________ >>Biopython-dev mailing list >>Biopython-dev@biopython.org >>http://biopython.org/mailman/listinfo/biopython-dev > Hello Jeff: Thanks for your email. I downloaded cvs version of biopython. I install numarray0.3.5. I get the following error message when I tried to install biopython with following command: python setup.py install building 'Bio.Tools.KDTree._KDTreecmodule' extension skipping Bio/Tools/KDTree/_KDTree.C (build/temp.linux-i686-2.2/_KDTree.o g -O3 -Wall -Wstrict-prototypes -fPIC -I/home/desas2/inclu de/python2.2 -c Bio/Tools/KDTree/_KDTree.swig.C -o build/temp.linux-i686-2.2/_KD Tree.swig.o Please let me know what else I need to install to fix this problem of install of cvs version of biopython. Thank you very much for your time. Dinakar -- Dinakar Desai, Ph.D Phone: 289-3972/266-2831 perl -e '$_ = "mqonx.zako\@ude";$_=~ tr /qnxzk\@.ue/npqmy.\@eu/; print' ---------------------- Everything should be made as simple as possible, but no simpler.-----Albert Einstein From Desai.Dinakar at mayo.edu Thu Jul 18 13:30:40 2002 From: Desai.Dinakar at mayo.edu (Dinakar Desai) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] need help with Genbank - additional error References: <3D36E6A1.1060509@mayo.edu> <20020718091900.B48356@springfield.stanford.edu> <3D36FA60.5080402@mayo.edu> Message-ID: <3D36FB40.6080508@mayo.edu> Dinakar Desai wrote: > Jeffrey Chang wrote: > >> The GenBank parser has gone through a few revisions to handle format >> changes since 1.00a4 was released. Try getting the latest version out >> of CVS (cvs.open-bio.org) and see if that fixes the problem. >> >> Otherwise, please send in a sample GenBank record that causes the >> parser to break. >> >> Jeff >> >> >> >> >> On Thu, Jul 18, 2002 at 11:02:41AM -0500, Dinakar Desai wrote: >> >>> Hello: >>> >>> I have install biopython1.004a and python 2.2.1 on linux box. I am >>> going through tutorial written by Brad et al. (very good work). >>> With following code I get trace back which I have pasted at the end. >>> Can someone help me with. I must be dong something wrong here. >>> >>> Thanks >>> >>> Dinakar >>> >>> 30 from Bio import GenBank >>> 31 record_file = open('record_file.seq', 'w+') >>> 32 record_parser = GenBank.FeatureParser() >>> 33 ncbi_dict = GenBank.NCBIDictionary() >>> 34 for id in titles: >>> 35 gb_seqrecord = ncbi_dict[id] >>> 36 record_file.write( gb_seqrecord) >>> 37 >>> 38 >>> 39 record_file.close() >>> 40 record_file = open('record_file.seq', 'r') >>> 41 gb_iter = GenBank.Iterator(record_file, record_parser) >>> 42 while 1: >>> 43 current_record = gb_iter.next() >>> 44 if current_record is None: >>> 45 break >>> 46 print current_record.seq >>> 47 print current_record.source >>> 48 print current_record.author >>> 49 record_file.close() >>> >>> >>> >>> Traceback (most recent call last): >>> File "./test_as.py", line 43, in ? >>> current_record = gb_iter.next() >>> File >>> "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", >>> linet >>> return self._parser.parse(File.StringHandle(data)) >>> File >>> "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", >>> linee >>> self._scanner.feed(handle, self._consumer) >>> File >>> "/home/desas2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", >>> lined >>> self._parser.parseFile(handle) >>> File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", >>> line 230, ie >>> self.parseString(fileobj.read()) >>> File "/home/desas2/lib/python2.2/site-packages/Martel/Parser.py", >>> line 258, ig >>> self._err_handler.fatalError(result) >>> File "/home/desas2/lib/python2.2/xml/sax/handler.py", line 38, in >>> fatalError >>> raise exception >>> Martel.Parser.ParserPositionException: error parsing at or beyond >>> character 55 >>> >>> >>> -- >>> >>> >>> _______________________________________________ >>> Biopython-dev mailing list >>> Biopython-dev@biopython.org >>> http://biopython.org/mailman/listinfo/biopython-dev >> >> > > Hello Jeff: > > Thanks for your email. I downloaded cvs version of biopython. I install > numarray0.3.5. I get the following error message when I tried to install > biopython with following command: > python setup.py install > > > building 'Bio.Tools.KDTree._KDTreecmodule' extension > skipping Bio/Tools/KDTree/_KDTree.C (build/temp.linux-i686-2.2/_KDTree.o > g -O3 -Wall -Wstrict-prototypes -fPIC -I/home/desas2/inclu > de/python2.2 -c Bio/Tools/KDTree/_KDTree.swig.C -o > build/temp.linux-i686-2.2/_KD > Tree.swig.o > > > Please let me know what else I need to install to fix this problem of > install of cvs version of biopython. > > Thank you very much for your time. > > Dinakar > > To follow up: I also had this error message at end. skipping Bio/Tools/KDTree/_KDTree.C (build/temp.linux-i686-2.2/_KDTree.o up-to-) gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -I/home/desas2/include/pytho Bio/Tools/KDTree/_KDTree.swig.C:748:42: Numeric/arrayobject.h: No such file or y error: command 'gcc' failed with exit status 1 Thanks Dinakar -- Dinakar Desai, Ph.D Phone: 289-3972/266-2831 perl -e '$_ = "mqonx.zako\@ude";$_=~ tr /qnxzk\@.ue/npqmy.\@eu/; print' ---------------------- Everything should be made as simple as possible, but no simpler.-----Albert Einstein From jchang at smi.stanford.edu Thu Jul 18 13:39:10 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] need help with Genbank - additional error In-Reply-To: <3D36FB40.6080508@mayo.edu>; from Desai.Dinakar@mayo.edu on Thu, Jul 18, 2002 at 12:30:40PM -0500 References: <3D36E6A1.1060509@mayo.edu> <20020718091900.B48356@springfield.stanford.edu> <3D36FA60.5080402@mayo.edu> <3D36FB40.6080508@mayo.edu> Message-ID: <20020718103910.A48653@springfield.stanford.edu> On Thu, Jul 18, 2002 at 12:30:40PM -0500, Dinakar Desai wrote: > > Thanks for your email. I downloaded cvs version of biopython. I install > > numarray0.3.5. I get the following error message when I tried to install > > biopython with following command: > > python setup.py install > > > > > > building 'Bio.Tools.KDTree._KDTreecmodule' extension > > skipping Bio/Tools/KDTree/_KDTree.C (build/temp.linux-i686-2.2/_KDTree.o > > g -O3 -Wall -Wstrict-prototypes -fPIC -I/home/desas2/inclu > > de/python2.2 -c Bio/Tools/KDTree/_KDTree.swig.C -o > > build/temp.linux-i686-2.2/_KD > > Tree.swig.o > > > > > > Please let me know what else I need to install to fix this problem of > > install of cvs version of biopython. You can safely ignore this error message. It is code in development for the next release of biopython and will not affect the GenBank package. In the setup.py file, comment out the lines at the end of the file that contain "KDTree": #Extension('Bio.Tools.KDTree._KDTreecmodule', # ["Bio/Tools/KDTree/_KDTree.C", # "Bio/Tools/KDTree/_KDTree.swig.C"], # libraries=["stdc++"] # ) Jeff From Desai.Dinakar at mayo.edu Thu Jul 18 14:54:02 2002 From: Desai.Dinakar at mayo.edu (Dinakar Desai) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] need help with Genbank - THANKS References: <3D36E6A1.1060509@mayo.edu> <20020718091900.B48356@springfield.stanford.edu> <3D36FA60.5080402@mayo.edu> <3D36FB40.6080508@mayo.edu> <20020718103910.A48653@springfield.stanford.edu> Message-ID: <3D370ECA.8050504@mayo.edu> Jeffrey Chang wrote: > On Thu, Jul 18, 2002 at 12:30:40PM -0500, Dinakar Desai wrote: > > You can safely ignore this error message. It is code in development > for the next release of biopython and will not affect the GenBank > package. In the setup.py file, comment out the lines at the end of > the file that contain "KDTree": > #Extension('Bio.Tools.KDTree._KDTreecmodule', > # ["Bio/Tools/KDTree/_KDTree.C", > # "Bio/Tools/KDTree/_KDTree.swig.C"], > # libraries=["stdc++"] > # ) > > Jeff > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev Hello Jeff and others: Thank you very much. That solved the problem. I am going through documents (produced by HappyDoc), can anyone please tell me how I could find all the connection between classes like class diagram. I have taken up small project to work with biopython. I thought, for me that is only way to learn biopython. In the beginning I may have more questions. please bear with me. Thank you. Dinakar -- Dinakar Desai, Ph.D Phone: 289-3972/266-2831 perl -e '$_ = "mqonx.zako\@ude";$_=~ tr /qnxzk\@.ue/npqmy.\@eu/; print' ---------------------- Everything should be made as simple as possible, but no simpler.-----Albert Einstein From jchang at smi.stanford.edu Sat Jul 20 19:26:41 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] Follow up to bug incoming/75 In-Reply-To: <3D349CF2.9030009@egcrc.net>; from daishi@egcrc.net on Tue, Jul 16, 2002 at 03:23:46PM -0700 References: <3D3357A0.3040806@egcrc.net> <20020716003216.B41639@springfield.stanford.edu> <3D349CF2.9030009@egcrc.net> Message-ID: <20020720162641.B56220@springfield.stanford.edu> Hi Daishi, I'm afraid that the algorithm I implemented for Bio.Align.fastpairwise just doesn't handle local alignments very well. There are a lot of boundary cases, and you have found one of them. To address this, I have implemented a new dynamic programming algorithm based on the Needleman-Wunsch algorithm that was implemented in Bio.Align.pairwise. I saved this as the module Bio.Align.pairwise2. Bio.Align.pairwise2 caches some gap scores, so that for affine gap penalties, it has the same asymptotic running time as Bio.Align.fastpairwise. Plus, it maintains more information in its data structure so it makes the traceback much easier to understand. I believe the code will be easier to maintain. I did some profiling, and it seems that the for Bio.Align.pairwise2 is slower than Bio.Align.fastpairwise, but the traceback is faster, which evens things out. Since this module replaces the functionality of Bio.Align.pairwise and Bio.Align.fastpairwise, I am going to deprecate them in future releases of Biopython. Please take a look at Bio.Align.pairwise2 and let me know if you find any problems! Thanks, Jeff On Tue, Jul 16, 2002 at 03:23:46PM -0700, daishi@egcrc.net wrote: > Jeffrey Chang wrote: > > Hi Daishi, > > > > Thanks for the bug report and patch. I will look into this soon. > > > > Jeff > > Please ignore the previous patch; it contains a bug. > I believe I now understand the purpose of L332-333; > I have reincorporated the functionality in a slightly > different way which works with my other modifications. > The new patch follows: > > *** /usr/local/src/biopython/Bio/Align/fastpairwise.py Tue Jul 9 15:08:53 2002 > --- fastpairwise.py Tue Jul 16 15:15:50 2002 > *************** > *** 302,308 **** > else: > # Since the length of the alignment is unknown, set an > # offset from the end of the alignment. > ! begin, end = 0, -len(seqA) > if not end: > end = None > x = seqA, seqB, score, begin, end, row, col, [] > --- 302,308 ---- > else: > # Since the length of the alignment is unknown, set an > # offset from the end of the alignment. > ! begin, end = None, -len(seqA) > if not end: > end = None > x = seqA, seqB, score, begin, end, row, col, [] > *************** > *** 326,341 **** > elif col < 0: > begin = row + 1 > for cseqA, cseqB, cbegin, taillen in path_cache[(row, col)]: > ! nbegin = begin > nseqA = cseqA[:-taillen] + seqA > nseqB = cseqB[:-taillen] + seqB > ! if nbegin < cbegin: > ! nbegin = cbegin > x = nseqA, nseqB, score, nbegin, end, -1, -1, path > in_process.append(x) > elif row < 0 and col < 0: > # This one is done. Put it into the tracebacks list and > # continue. > tracebacks.append((seqA, seqB, score, begin, end)) > path.pop() # Don't cache the last step. > # Update the cache. > --- 326,346 ---- > elif col < 0: > begin = row + 1 > for cseqA, cseqB, cbegin, taillen in path_cache[(row, col)]: > ! if begin: > ! nbegin = begin > ! else: > ! nbegin = cbegin > nseqA = cseqA[:-taillen] + seqA > nseqB = cseqB[:-taillen] + seqB > ! # if nbegin < cbegin: > ! # nbegin = cbegin > x = nseqA, nseqB, score, nbegin, end, -1, -1, path > in_process.append(x) > elif row < 0 and col < 0: > # This one is done. Put it into the tracebacks list and > # continue. > + if not begin: > + begin = 0 > tracebacks.append((seqA, seqB, score, begin, end)) > path.pop() # Don't cache the last step. > # Update the cache. > *************** > *** 347,360 **** > elif row < 0: > nseqA = gap_char + seqA > nseqB = sequenceB[col:col+1] + seqB > ! if not global_alignment: > begin = col + 1 > x = nseqA, nseqB, score, begin, end, row, col-1, path > in_process.append(x) > elif col < 0: > nseqA = sequenceA[row:row+1] + seqA > nseqB = gap_char + seqB > ! if not global_alignment: > begin = row + 1 > x = nseqA, nseqB, score, begin, end, row-1, col, path > in_process.append(x) > --- 352,365 ---- > elif row < 0: > nseqA = gap_char + seqA > nseqB = sequenceB[col:col+1] + seqB > ! if not (global_alignment or begin): > begin = col + 1 > x = nseqA, nseqB, score, begin, end, row, col-1, path > in_process.append(x) > elif col < 0: > nseqA = sequenceA[row:row+1] + seqA > nseqB = gap_char + seqB > ! if not (global_alignment or begin): > begin = row + 1 > x = nseqA, nseqB, score, begin, end, row-1, col, path > in_process.append(x) From katel at worldpath.net Tue Jul 23 18:29:58 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] MetaTool References: <3D3357A0.3040806@egcrc.net> <20020716003216.B41639@springfield.stanford.edu> <3D349CF2.9030009@egcrc.net> <20020720162641.B56220@springfield.stanford.edu> Message-ID: <004801c23298$7b93d960$08fea8c0@pcklindner> I plan to fix metatool in a day or two when I go to the lake island where I have my new linux system to run the tests It looks like there is an extraneous file that is not part of the tests. It should not cause tests to fail but it may confuse users. Cayte> > > > > On Tue, Jul 16, 2002 at 03:23:46PM -0700, daishi@egcrc.net wrote: > > Jeffrey Chang wrote: > > > Hi Daishi, > > > > > > Thanks for the bug report and patch. I will look into this soon. > > > > > > Jeff > > > > Please ignore the previous patch; it contains a bug. > > I believe I now understand the purpose of L332-333; > > I have reincorporated the functionality in a slightly > > different way which works with my other modifications. > > The new patch follows: > > > > *** /usr/local/src/biopython/Bio/Align/fastpairwise.py Tue Jul 9 15:08:53 2002 > > --- fastpairwise.py Tue Jul 16 15:15:50 2002 > > *************** > > *** 302,308 **** > > else: > > # Since the length of the alignment is unknown, set an > > # offset from the end of the alignment. > > ! begin, end = 0, -len(seqA) > > if not end: > > end = None > > x = seqA, seqB, score, begin, end, row, col, [] > > --- 302,308 ---- > > else: > > # Since the length of the alignment is unknown, set an > > # offset from the end of the alignment. > > ! begin, end = None, -len(seqA) > > if not end: > > end = None > > x = seqA, seqB, score, begin, end, row, col, [] > > *************** > > *** 326,341 **** > > elif col < 0: > > begin = row + 1 > > for cseqA, cseqB, cbegin, taillen in path_cache[(row, col)]: > > ! nbegin = begin > > nseqA = cseqA[:-taillen] + seqA > > nseqB = cseqB[:-taillen] + seqB > > ! if nbegin < cbegin: > > ! nbegin = cbegin > > x = nseqA, nseqB, score, nbegin, end, -1, -1, path > > in_process.append(x) > > elif row < 0 and col < 0: > > # This one is done. Put it into the tracebacks list and > > # continue. > > tracebacks.append((seqA, seqB, score, begin, end)) > > path.pop() # Don't cache the last step. > > # Update the cache. > > --- 326,346 ---- > > elif col < 0: > > begin = row + 1 > > for cseqA, cseqB, cbegin, taillen in path_cache[(row, col)]: > > ! if begin: > > ! nbegin = begin > > ! else: > > ! nbegin = cbegin > > nseqA = cseqA[:-taillen] + seqA > > nseqB = cseqB[:-taillen] + seqB > > ! # if nbegin < cbegin: > > ! # nbegin = cbegin > > x = nseqA, nseqB, score, nbegin, end, -1, -1, path > > in_process.append(x) > > elif row < 0 and col < 0: > > # This one is done. Put it into the tracebacks list and > > # continue. > > + if not begin: > > + begin = 0 > > tracebacks.append((seqA, seqB, score, begin, end)) > > path.pop() # Don't cache the last step. > > # Update the cache. > > *************** > > *** 347,360 **** > > elif row < 0: > > nseqA = gap_char + seqA > > nseqB = sequenceB[col:col+1] + seqB > > ! if not global_alignment: > > begin = col + 1 > > x = nseqA, nseqB, score, begin, end, row, col-1, path > > in_process.append(x) > > elif col < 0: > > nseqA = sequenceA[row:row+1] + seqA > > nseqB = gap_char + seqB > > ! if not global_alignment: > > begin = row + 1 > > x = nseqA, nseqB, score, begin, end, row-1, col, path > > in_process.append(x) > > --- 352,365 ---- > > elif row < 0: > > nseqA = gap_char + seqA > > nseqB = sequenceB[col:col+1] + seqB > > ! if not (global_alignment or begin): > > begin = col + 1 > > x = nseqA, nseqB, score, begin, end, row, col-1, path > > in_process.append(x) > > elif col < 0: > > nseqA = sequenceA[row:row+1] + seqA > > nseqB = gap_char + seqB > > ! if not (global_alignment or begin): > > begin = row + 1 > > x = nseqA, nseqB, score, begin, end, row-1, col, path > > in_process.append(x) > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > > From katel at worldpath.net Wed Jul 24 22:26:14 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] Ais example Message-ID: <001f01c23382$a77198c0$a8dc85d0@pcklindner> I just checked an example program in Ais.Examples. It tests a mutation from SNP against a tryptophanyl-tRNA synthetase . It triggered valid mismatches and 1 false trigger but I display the weasel words suspicious sequence. I need to tweak parameters and experiment a little. Ais runs slow because it uses a live random generator. After xchanging email with Gavin I decided I'll make the randomizer selectable next. The true randomizer is for when you have time or when someone shouts "Artefact!". I set the server to www.random.org because HotBits has a limit on bytes u can download. Cayte From Y.Benita at pharm.uu.nl Wed Jul 31 05:44:45 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] The signal module on the Mac Message-ID: Hi all, I am trying to put together a Macos X biopython for MacPython (not the command line python). On the Mac there is no signal module and therefore many modules fail (import error). The addition of the signal module is new because I don't remember having those errors in 1.004. Anyway, I asked for some help on the MacPython list and got that from jack Jansen: How to fix this depends on how the signal module is used. If it's used to detect "unexpected" errors you may be able to simply do away with it (or add a lookalike module that does nothing). If it is used to detect "expected" errors (like floating overflow or underflow) you may have more of a problem. What do you guys think: Remove it and ignore the signal module or try to replace it with something else? Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University